CrystalMaker Guide: Bond Specifications

You can define bonds on an atom-by-atom basis, you can request bonds between particular atom types up to a maximum distance, or CrystalMaker can automatically generate bonds for you.

Defining Individual Bonds

You can use the Add/Delete Bond Tool to generate a bond between two specified atoms. With this tool selected, click on two atoms in the structure. If the atoms are already bonded to each other, their bond will be deleted; otherwise, a new bond will be created between them.

If you hold down the shift key as you click the second atom, CrystalMaker will generate similar bonds throughout the plotted structure.

Defining Specific Bonds

You can use the Edit Bond Specifications dialog (Edit > Bond Specs) to request gobal bond specifications, on the basis of atom types (element symbols) and their maximum separations.

Automatic Bond Generation

You can use the Transform >Generate Bonds command to search through the structure and generate bonds for all atoms whose interatomic separations lie within 15% of the sum of their radii (*)

Note: you may need to edit atomic radii for this method to work. In some cases you may wish to import a new Element Table (Edit > Elements) - e.g., if you usually work with ionic structures but wish to plot an organic structures, you might want to temporarily use atomic radii corresponding to those found in organic structures.

(*) CrystalMaker versions 4.0.4, and later, use standard organic bond distances, when searching for bonds as part of the Auto Bond Search command - these distances are independent of the values used in the Elements Table, meaning that you can work with organic structures, without necessarily having to reset your current elements table.

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